In order to support virtual prototype of flight control system (FCS-VP ) design, to shorten the design period and reduce the cost of flight control system incurred by five commercial software, such as physical prototype, integrated Rhapsody, Matlab／Simulink, VC++, Doors, and Oracle, the virtual prototype design environments of flight control system (FCS-VPDE) is researched. FCS-VPDE contains fourlayer: model design layer, virtual component design layer, virtual prototype integration layer and scheduling management layer. In order to test the performance of FCS-VPDE, a Micro air vehicle′s FCS-VP is designed, and co-simulation is conducted for the FCS-VP. The experimental results demonstrate that FCS- VPDE is suitable for different particle size of the FCS-VP design, which can improve the efficiency of the flight control system design and support various aircraft FCS-VP design.